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protein complexes detecting for pharmaceutical processes control via Spectral clustering with local connectivity kernel

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Protein complexes detecting for pharmaceutical processes con...

Physiochemcial Features Study of protein complexes

第35届中国过程控制会议

作者： Wenjie Guo Wei Zeng Feng Li Xinggao Liu College of Control Science and Engineering Zhejiang University Yi Chang HEC Biochemical Pharmaceutical Co. Ltd.

Pharmacy is a complex process involving many variables. Among them, various proteins produced in the biological reaction process and protein complexes of them have an important influence on the control of pharmaceutical process. In addition, detection of protein complexes is also the most essential and fundamental problem in most Bionic manufacturing industry. However, most existing clustering technical for protein complexes detection focus primarily on the local information of the protein-protein interaction networks(PPI), which leads to the global distribution between proteins is lost and some protein complexes are further missed. Therefore, a method namely spectral clustering with improved connectivity kernel(SPICK) is proposed to detect protein complexes based on both local and global information of the protein-protein interaction networks. In SPICK, the improved connectivity kernel considers both Euclidean distance and connectivity kernel to calculate the affinity matrix, which combines local information with global distribution of PPI effectively. Experimental results show that our method performs better in comparison to existing protein complexes techniques.

关键词： protein complexes spectral clustering global distribution connectivity kernel PPI

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Physiochemcial Features Study of Protein Complexes

CNKSR2 interactome analysis indicates its association with the centrosome/microtubule system

2011 4th IEEE International Conference on Computer Science and Information Technology(ICCSIT 2011)

作者： Chien-Hung Huang Kun-Ting Chao Ka-Lok Ng Department of Computer Science and Information Engineering National Formosa University Department of Biomedical Informatics Asia University

ISBN: (纸本)9781612848334

It is known that protein complexes play important roles in many cellular *** protein complex prediction methods are based on the identification of pseudocliques,and dense protein-protein interaction（PPI） *** acids’ physiochemical properties are not generally used in the feature representation of protein *** results of the physiochemical properties study for human protein complexes are *** independent statistical methods,logistic regression（LR） and principle component analysis（PCA）,are carried out to determine the major features.A 6fold cross-validation test is performed based on the features to test the classification accuracy of the Support Vector Machine（SVM）.It is found that the hydrophoblic and hydrophilic serve as additional important feature besides PPI.

关键词： protein complexes physiochemical properties principle component analysis logistic regression support vector machine

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Neural Regeneration Research 2025年第8期20卷 2420-2432页

作者： Lin Yin Yalan Xu Jie Mu Yu Leng Lei Ma Yu Zheng Ruizhi Li Yin Wang Peifeng Li Hai Zhu Dong Wang Jing Li Institute for Translational Medicine The Affiliated Hospital of Qingdao UniversityMedical CollegeQingdao UniversityQingdaoShandong ProvinceChina School of Basic Medicine Qingdao UniversityQingdaoShandong ProvinceChina College of Life Sciences and School of PharmacyMedical CollegeQingdao UniversityQingdaoShandong ProvinceChina Department of Urology Qingdao Municipal Hospital Affiliated to Qingdao UniversityQingdaoShandong ProvinceChina

The protein connector enhancer of kinase suppressor of Ras 2(CNKSR2),present in both the postsynaptic density and cytoplasm of neurons,is a scaffolding protein with several protein-binding *** of the CNKSR2 gene have been implicated in neurodevelopmental disorders,particularly intellectual disability,although the precise mechanism involved has not yet been fully *** has demonstrated that CNKSR2 plays a role in facilitating the localization of postsynaptic density protein complexes to the membrane,thereby influencing synaptic signaling and the morphogenesis of dendritic ***,the function of CNKSR2 in the cytoplasm remains to be *** this study,we used immunoprecipitation and high-resolution liquid chromatography-mass spectrometry to identify the interactors of *** a combination of bioinformatic analysis and cytological experiments,we found that the CNKSR2 interactors were significantly enriched in the proteome of the *** also showed that CNKSR2 interacted with the microtubule protein DYNC1H1 and with the centrosome marker *** colocalization analysis confirmed the centrosomal localization of *** we downregulated CNKSR2 expression in mouse neuroblastoma cells(Neuro 2A),we observed significant changes in the expression of numerous centrosomal *** manipulation also affected centrosome-related functions,including cell size and shape,cell proliferation,and ***,we found that CNKSR2 interactors were highly enriched in de novo variants associated with intellectual disability and autism spectrum *** findings establish a connection between CNKSR2 and the centrosome,and offer new insights into the underlying mechanisms of neurodevelopmental disorders.

关键词： autism spectrum disorder centrosome CNKSR2 intellectual disability interactome mass spectrometry microtubule neurodevelopmental disease protein complexes protein-protein interactions

Towards dynamic structure of biological complexes at atomic resolution by cryo-EM

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Chinese Physics B 2018年第6期27卷 35-46页

作者： Kai Zhang The Medical Research Council Laboratory of Molecular Biology Cambridge CB2 0QH United Kingdo

Cryo-electron microscopy makes use of transmission electron microscopy to image vitrified biological samples and reconstruct their three-dimensional structures from two-dimensional projections via computational approaches. After over40 years of development, this technique is now reaching its zenith and reforming the research paradigm of modern structural biology. It has been gradually taking over X-ray crystallography as the mainstream method. In this review, we briefly introduce the history of cryo-EM, recent technical development and its potential power to reveal dynamic structures. The technical barriers and possible approaches to tackle the upcoming challenges are discussed.

关键词： cryo-electron microscopy protein complexes three-dimensional reconstruction dynamic structures probabilistic conformational spaces

protein Interactome Analysis for Countering Pathogen Drug Resistance

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Journal of Computer Science & Technology 2010年第1期25卷 124-130页

作者： Limsoon Wong Guimei Liu School of Computing National University of Singapore

Drug-resistant varieties of pathogens are now a recognized global threat. Insights into the routes for drug resistance in these pathogens are critical for developing more effective antibacterial drugs. A systems-level analysis of the genes, proteins, and interactions involved is an important step to gaining such insights. This paper discusses some of the computational challenges that must be surmounted to enable such an analysis; viz., unreliability of bacterial interactome maps, paucity of bacterial interactome maps, and identification of pathways to bacterial drug resistance.

关键词： protein complexes protein interactomes drug resistance infectious diseases

The DUF579 proteins GhIRX15s regulate cotton fiber development by interacting with proteins involved in xylan synthesis

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The Crop Journal 2024年第4期12卷 1112-1125页

作者： Mengyun Li Feng Chen Jingwen Luo Yanan Gao Jinglong Cai Wei Zeng Monika S.Doblin Gengqing Huang Wenliang Xu Hubei Key Laboratory of Genetic Regulation and Integrative Biology School of Life SciencesCentral China Normal UniversityWuhan 430079HubeiChina Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation School of Life SciencesTaizhou UniversityTaizhou 318000ZhejiangChina La Trobe Institute for Sustainable Agriculture&Food School of AgricultureBiomedicine and EnvironmentLa Trobe UniversityBundooraVIC 3086Australia

Cotton provides the most abundant natural fiber for the textile *** mature cotton fiber largely consists of secondary cell walls with the highest proportion of cellulose and a small amount of hemicellulose and *** dissect the roles of hemicellulosic polysaccharides during fiber development,four IRREGULAR XYLEM 15(IRX15)genes,GhIRX15-1/-2/-3/-4,were functionally characterized in *** genes encode DUF579 domain-containing proteins,which are homologs of AtIRX15 involved in xylan *** four GhIRX15 genes were predominantly expressed during fiber secondary wall thickening,and the encoded proteins were localized to the Golgi *** GhIRX15 gene could restore the xylan deficient phenotype in the Arabidopsis irx15irx15l double *** of GhIRX15s in cotton resulted in shorter mature fibers with a thinner cell wall and reduced cellulose content as compared to the wild ***,GhIRX15-2 and GhIRX15-4 formed homodimers and *** addition,the GhIRX15s showed physical interaction with glycosyltransferases GhGT43C,GhGT47A and GhGT47B,which are responsible for synthesis of the xylan backbone and reducing end ***,the GhIRX15s can form heterocomplexes with enzymes involved in xylan modification and side chain synthesis,such as GhGUX1/2,GhGXM1/2 and *** findings suggest that GhIRX15s participate in fiber xylan biosynthesis and modulate fiber development via forming large multiprotein complexes.

关键词： Cotton fiber Xylan biosynthesis GhIRX15s protein-protein interaction protein complexes

PDRG1 at the interface between intermediary metabolism and oncogenesis

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World Journal of Biological Chemistry 2017年第4期8卷 175-186页

作者： Maríaángeles Pajares Department of Chemical and Physical Biology Centro de Investigaciones Biológicas(CSIC)Madrid 28040Spain Instituto de Investigación Sanitaria La Paz(IdiPAZ) Madrid 28046Spain

PDRG1 is a small oncogenic protein of 133 residues. In normal human tissues, the p53 and DNA damageregulated gene 1(PDRG1) gene exhibits maximal expression in the testis and minimal levels in the liver. Increased expression has been detected in several tumor cells and in response to genotoxic stress. High-throughput studies identified the PDRG1 protein in a variety of macromolecular complexes involved in processes that are altered in cancer cells. For example, this oncogene has been found as part of the RNA polymerase Ⅱ complex, the splicing machinery and nutrient sensing machinery, although its role in these complexes remains unclear. More recently, the PDRG1 protein was found as an interaction target for the catalytic subunits of methionine adenosyltransferases. These enzymes synthesize S-adenosylmethionine, the methyl donor for, among others, epigenetic methylations that occur on the DNA and histones. In fact, downregulation of S-adenosylmethionine synthesis is the first functional effect directly ascribed to PDRG1. The existence of global DNA hypomethylation, together with increased PDRG1 expression, in many tumor cells highlights the importance of this interaction as one of the putative underlying causes for cell transformation. Here, we will review the accumulated knowledge on this oncogene, emphasizing the numerous aspects that remain to be explored.

关键词： Epigenetic modifications Glutathione Methylation Oncogenes Intermediary metabolism p53 and DNA damage-regulated gene 1 protein complexes R2TP/prefoldin complex S-adenosylmethionine synthesis Redox stress

Phosphoprotein phosphatase 1-interacting proteins as therapeutic targets in prostate cancer

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World Journal of Pharmacology 2014年第4期3卷 120-139页

作者： Juliana Felgueiras Margarida Fardilha Laboratory of Signal Transduction Centre for Cell Biology Biology Department and Health Sciences Department University of Aveiro Campus de Santiago 3810-193 Aveiro Portugal

Prostate cancer is a major public health concern world-wide, being one of the most prevalent cancers in men. Great improvements have been made both in terms of early diagnosis and therapeutics. However, there is still an urgent need for reliable biomarkers that could overcome the lack of cancer-specifcity of prostate-specifc antigen, as well as alternative therapeutic targets for advanced metastatic cases. Reversible phosphorylation of proteins is a post-translational modifcation critical to the regulation of numerous cellular processes. Phosphoprotein phosphatase 1 （PPP1） is a major serine/threonine phos-phatase, whose specifcity is determined by its interacting proteins. These interactors can be PPP1 substrates, regulators, or even both. Deregulation of this protein-protein interaction network alters cell dynamics and underlies the development of several cancer hallmarks. Therefore, the identification of PPP1 interactome in specific cellular context is of crucial importance. The knowledge on PPP1 complexes in prostate cancer remains scarce, with only 4 holoenzymes characterized in human prostate cancer models. However, an increasing number of PPP1 interactors have been identifed as expressed in human prostate tissue, including the tumor suppressors TP53 and RB1. Efforts should be made in order to identify the role of such proteins in prostate carcinogenesis, since only 26 have yet well-recognized roles. Here, we revise literature and human protein databases to provide an in-depth knowledge on the biological significance of PPP1 complexes in human prostate carcinogenesis and their potential use as therapeutic targets for the development of new therapies for prostate cancer.

关键词： Prostate cancer Reversible phosphorylation Phosphoprotein phosphatase 1 Phosphoprotein phosphatase 1-interacting proteins protein complexes Therapeutic targets

Two-dimensional Native/SDS PAGE Proteomic Approach for Cytosolic and Iron-dependent protein Complexome in Escherichia coli

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Two-dimensional Native/SDS PAGE Proteomic Approach for Cytos...